Multiple sequence alignment - TraesCS4D01G123100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4D01G123100 chr4D 100.000 4259 0 0 1 4259 107440927 107436669 0.000000e+00 7866.0
1 TraesCS4D01G123100 chr4D 92.593 54 4 0 3661 3714 107437035 107437088 1.270000e-10 78.7
2 TraesCS4D01G123100 chr4D 87.879 66 8 0 3828 3893 107437202 107437267 1.270000e-10 78.7
3 TraesCS4D01G123100 chr4D 91.667 48 2 2 348 394 122695630 122695584 9.880000e-07 65.8
4 TraesCS4D01G123100 chr4A 95.796 1998 42 15 671 2631 468752181 468754173 0.000000e+00 3186.0
5 TraesCS4D01G123100 chr4A 96.960 1217 26 3 2516 3728 468754171 468755380 0.000000e+00 2032.0
6 TraesCS4D01G123100 chr4A 88.000 325 27 3 3906 4218 468755542 468755866 1.450000e-99 374.0
7 TraesCS4D01G123100 chr4A 87.603 121 6 4 3819 3934 468755400 468755516 9.610000e-27 132.0
8 TraesCS4D01G123100 chr4B 95.065 1925 71 8 187 2102 169582211 169584120 0.000000e+00 3007.0
9 TraesCS4D01G123100 chr4B 95.840 1803 47 12 2099 3888 169590571 169592358 0.000000e+00 2889.0
10 TraesCS4D01G123100 chr4B 97.551 245 6 0 3843 4087 169592365 169592609 1.830000e-113 420.0
11 TraesCS4D01G123100 chr4B 92.896 183 11 2 4072 4253 169595897 169596078 9.080000e-67 265.0
12 TraesCS4D01G123100 chr4B 93.750 48 3 0 344 391 18087563 18087516 5.910000e-09 73.1
13 TraesCS4D01G123100 chr4B 86.885 61 8 0 3666 3726 169592358 169592298 7.640000e-08 69.4
14 TraesCS4D01G123100 chr4B 97.143 35 1 0 402 436 581907178 581907144 4.600000e-05 60.2
15 TraesCS4D01G123100 chr7A 81.648 267 43 5 3990 4255 204736741 204737002 2.580000e-52 217.0
16 TraesCS4D01G123100 chr7A 91.139 79 5 2 461 537 335980813 335980735 5.820000e-19 106.0
17 TraesCS4D01G123100 chr7A 89.610 77 7 1 462 537 34048461 34048385 3.510000e-16 97.1
18 TraesCS4D01G123100 chr7A 95.349 43 2 0 349 391 690660162 690660204 7.640000e-08 69.4
19 TraesCS4D01G123100 chr6B 81.496 254 37 8 4003 4254 636788473 636788228 2.600000e-47 200.0
20 TraesCS4D01G123100 chr6B 93.258 89 5 1 2554 2641 583192122 583192034 3.460000e-26 130.0
21 TraesCS4D01G123100 chr6A 81.526 249 38 6 4012 4258 504476031 504475789 9.340000e-47 198.0
22 TraesCS4D01G123100 chr6A 92.000 75 4 2 461 534 146554563 146554490 2.090000e-18 104.0
23 TraesCS4D01G123100 chr5D 81.395 258 34 11 3996 4248 63508783 63508535 9.340000e-47 198.0
24 TraesCS4D01G123100 chr1D 83.258 221 32 4 4002 4220 226450032 226449815 9.340000e-47 198.0
25 TraesCS4D01G123100 chr1D 84.568 162 21 2 543 704 46634624 46634467 1.590000e-34 158.0
26 TraesCS4D01G123100 chr1D 87.786 131 15 1 552 682 387944782 387944911 7.380000e-33 152.0
27 TraesCS4D01G123100 chr1D 97.561 41 1 0 351 391 462149387 462149427 2.120000e-08 71.3
28 TraesCS4D01G123100 chr1D 93.617 47 0 2 348 393 133566065 133566021 2.750000e-07 67.6
29 TraesCS4D01G123100 chr5B 82.589 224 35 4 3999 4220 489306571 489306350 1.210000e-45 195.0
30 TraesCS4D01G123100 chr5B 88.636 88 9 1 2554 2641 541337658 541337744 5.820000e-19 106.0
31 TraesCS4D01G123100 chr5B 91.026 78 3 4 462 536 43191407 43191483 7.530000e-18 102.0
32 TraesCS4D01G123100 chr5B 89.744 78 7 1 461 537 383538772 383538849 9.750000e-17 99.0
33 TraesCS4D01G123100 chr5B 81.111 90 5 4 344 433 484883278 484883355 1.280000e-05 62.1
34 TraesCS4D01G123100 chr5B 81.928 83 3 3 351 433 224323151 224323221 4.600000e-05 60.2
35 TraesCS4D01G123100 chr1A 82.883 222 33 5 4002 4220 293712667 293712448 1.210000e-45 195.0
36 TraesCS4D01G123100 chr2B 85.806 155 16 5 551 704 50021641 50021492 4.410000e-35 159.0
37 TraesCS4D01G123100 chr2B 90.789 76 5 2 462 535 37357144 37357069 2.710000e-17 100.0
38 TraesCS4D01G123100 chr2B 95.455 44 2 0 348 391 133007607 133007650 2.120000e-08 71.3
39 TraesCS4D01G123100 chr2B 94.737 38 2 0 2563 2600 557234812 557234849 4.600000e-05 60.2
40 TraesCS4D01G123100 chr6D 84.177 158 16 7 551 704 2364344 2364192 1.230000e-30 145.0
41 TraesCS4D01G123100 chr6D 90.667 75 5 2 462 535 73497327 73497400 9.750000e-17 99.0
42 TraesCS4D01G123100 chr3D 83.766 154 21 3 551 704 11442710 11442561 4.440000e-30 143.0
43 TraesCS4D01G123100 chr3D 83.871 155 17 8 552 704 419520644 419520792 1.600000e-29 141.0
44 TraesCS4D01G123100 chr3D 88.333 60 3 3 531 590 388381876 388381821 7.640000e-08 69.4
45 TraesCS4D01G123100 chr3A 83.439 157 22 2 548 704 169849408 169849560 4.440000e-30 143.0
46 TraesCS4D01G123100 chr3A 95.122 41 2 0 3823 3863 616726928 616726888 9.880000e-07 65.8
47 TraesCS4D01G123100 chr3B 83.660 153 22 3 552 704 665261474 665261325 1.600000e-29 141.0
48 TraesCS4D01G123100 chr3B 88.679 53 3 3 2560 2611 685661501 685661451 1.280000e-05 62.1
49 TraesCS4D01G123100 chr5A 94.203 69 3 1 462 529 382336374 382336306 2.090000e-18 104.0
50 TraesCS4D01G123100 chr7D 92.857 70 4 1 461 529 173020099 173020030 2.710000e-17 100.0
51 TraesCS4D01G123100 chr7D 97.619 42 1 0 2561 2602 506007045 506007004 5.910000e-09 73.1
52 TraesCS4D01G123100 chr7D 90.741 54 2 2 402 454 638257223 638257172 7.640000e-08 69.4
53 TraesCS4D01G123100 chr7D 100.000 31 0 0 406 436 60501306 60501336 1.650000e-04 58.4
54 TraesCS4D01G123100 chr2D 90.789 76 3 4 462 535 100188276 100188203 9.750000e-17 99.0
55 TraesCS4D01G123100 chr2D 95.455 44 2 0 348 391 81297952 81297995 2.120000e-08 71.3
56 TraesCS4D01G123100 chr2D 97.368 38 1 0 2563 2600 476352591 476352628 9.880000e-07 65.8
57 TraesCS4D01G123100 chr2A 88.406 69 2 5 524 588 11993539 11993605 1.270000e-10 78.7
58 TraesCS4D01G123100 chr2A 95.455 44 2 0 348 391 81752320 81752363 2.120000e-08 71.3
59 TraesCS4D01G123100 chrUn 89.286 56 3 3 3815 3867 399069397 399069452 2.750000e-07 67.6
60 TraesCS4D01G123100 chrUn 89.286 56 3 3 3815 3867 467735075 467735020 2.750000e-07 67.6
61 TraesCS4D01G123100 chrUn 89.286 56 3 3 3815 3867 474544541 474544596 2.750000e-07 67.6
62 TraesCS4D01G123100 chrUn 97.297 37 0 1 402 438 11966348 11966383 1.280000e-05 62.1
63 TraesCS4D01G123100 chrUn 97.297 37 0 1 402 438 12055784 12055819 1.280000e-05 62.1
64 TraesCS4D01G123100 chrUn 97.297 37 0 1 402 438 12157463 12157428 1.280000e-05 62.1
65 TraesCS4D01G123100 chr7B 95.238 42 2 0 2561 2602 11016425 11016466 2.750000e-07 67.6
66 TraesCS4D01G123100 chr1B 93.182 44 3 0 3823 3866 65704495 65704452 9.880000e-07 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G123100 chr4D 107436669 107440927 4258 True 7866.000000 7866 100.00000 1 4259 1 chr4D.!!$R1 4258
1 TraesCS4D01G123100 chr4A 468752181 468755866 3685 False 1431.000000 3186 92.08975 671 4218 4 chr4A.!!$F1 3547
2 TraesCS4D01G123100 chr4B 169582211 169584120 1909 False 3007.000000 3007 95.06500 187 2102 1 chr4B.!!$F1 1915
3 TraesCS4D01G123100 chr4B 169590571 169596078 5507 False 1191.333333 2889 95.42900 2099 4253 3 chr4B.!!$F2 2154

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
162 163 0.035458 TCACCACACACACACACACA 59.965 50.000 0.00 0.0 0.00 3.72 F
163 164 0.167908 CACCACACACACACACACAC 59.832 55.000 0.00 0.0 0.00 3.82 F
326 327 0.451783 CGCTAATGCCCAGTTCAACC 59.548 55.000 0.00 0.0 35.36 3.77 F
561 565 1.403780 CGTTTTCAGGTACTCCCTCCG 60.404 57.143 0.00 0.0 43.86 4.63 F
1887 1910 1.451207 CGGGTTTGATGATCGGCCA 60.451 57.895 2.24 0.0 0.00 5.36 F
2197 2243 4.378874 GCGATCATTAGGCATTTCTTAGGC 60.379 45.833 0.00 0.0 0.00 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2019 2042 1.202076 GCGAGAATTAAGCAGTGCCAC 60.202 52.381 12.58 0.00 0.00 5.01 R
2140 2186 4.582701 AGAGTCTCAGCCTAATGATTCG 57.417 45.455 1.94 0.00 0.00 3.34 R
2204 2250 8.408043 TCAAAGCTGGAATTCTGAAATCTTAA 57.592 30.769 5.23 0.00 0.00 1.85 R
2518 2564 3.197549 TGCACAACATCTATCTACCAGCA 59.802 43.478 0.00 0.00 0.00 4.41 R
2961 3136 0.036448 TATCCTCGTAGGGGAGCTCG 59.964 60.000 7.83 0.00 35.59 5.03 R
3748 3934 5.818136 TTTAGCCATTTCGGAGAAATGAG 57.182 39.130 27.34 20.19 45.90 2.90 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.323629 ACATACCACCAACCAGACCG 59.676 55.000 0.00 0.00 0.00 4.79
20 21 1.024579 CATACCACCAACCAGACCGC 61.025 60.000 0.00 0.00 0.00 5.68
21 22 2.193087 ATACCACCAACCAGACCGCC 62.193 60.000 0.00 0.00 0.00 6.13
22 23 3.953775 CCACCAACCAGACCGCCT 61.954 66.667 0.00 0.00 0.00 5.52
23 24 2.589157 CCACCAACCAGACCGCCTA 61.589 63.158 0.00 0.00 0.00 3.93
24 25 1.375523 CACCAACCAGACCGCCTAC 60.376 63.158 0.00 0.00 0.00 3.18
25 26 1.535687 ACCAACCAGACCGCCTACT 60.536 57.895 0.00 0.00 0.00 2.57
26 27 1.218316 CCAACCAGACCGCCTACTC 59.782 63.158 0.00 0.00 0.00 2.59
27 28 1.541310 CCAACCAGACCGCCTACTCA 61.541 60.000 0.00 0.00 0.00 3.41
28 29 0.537188 CAACCAGACCGCCTACTCAT 59.463 55.000 0.00 0.00 0.00 2.90
29 30 0.537188 AACCAGACCGCCTACTCATG 59.463 55.000 0.00 0.00 0.00 3.07
30 31 1.330655 ACCAGACCGCCTACTCATGG 61.331 60.000 0.00 0.00 0.00 3.66
31 32 1.227380 CAGACCGCCTACTCATGGC 60.227 63.158 0.00 0.00 46.42 4.40
36 37 3.255032 GCCTACTCATGGCCCCAT 58.745 61.111 0.00 0.00 44.32 4.00
48 49 4.073201 CCCCATGTGGCTAGAGGT 57.927 61.111 0.00 0.00 0.00 3.85
49 50 1.528824 CCCCATGTGGCTAGAGGTG 59.471 63.158 0.00 0.00 0.00 4.00
50 51 1.153086 CCCATGTGGCTAGAGGTGC 60.153 63.158 0.00 0.00 0.00 5.01
51 52 1.630126 CCCATGTGGCTAGAGGTGCT 61.630 60.000 0.00 0.00 0.00 4.40
52 53 0.179062 CCATGTGGCTAGAGGTGCTC 60.179 60.000 0.00 0.00 0.00 4.26
53 54 0.829333 CATGTGGCTAGAGGTGCTCT 59.171 55.000 0.00 0.00 43.83 4.09
54 55 1.209019 CATGTGGCTAGAGGTGCTCTT 59.791 52.381 0.00 0.00 41.50 2.85
55 56 0.610174 TGTGGCTAGAGGTGCTCTTG 59.390 55.000 0.00 0.00 41.50 3.02
67 68 3.184683 CTCTTGCACGAGCCTCGC 61.185 66.667 15.20 0.00 45.12 5.03
68 69 4.742201 TCTTGCACGAGCCTCGCC 62.742 66.667 15.20 6.22 45.12 5.54
94 95 2.199535 CCCCCTTGGCCATCCATC 59.800 66.667 6.09 0.00 43.05 3.51
95 96 2.397902 CCCCCTTGGCCATCCATCT 61.398 63.158 6.09 0.00 43.05 2.90
96 97 1.067762 CCCCCTTGGCCATCCATCTA 61.068 60.000 6.09 0.00 43.05 1.98
97 98 0.852842 CCCCTTGGCCATCCATCTAA 59.147 55.000 6.09 0.00 43.05 2.10
98 99 1.217689 CCCCTTGGCCATCCATCTAAA 59.782 52.381 6.09 0.00 43.05 1.85
99 100 2.310538 CCCTTGGCCATCCATCTAAAC 58.689 52.381 6.09 0.00 43.05 2.01
100 101 2.310538 CCTTGGCCATCCATCTAAACC 58.689 52.381 6.09 0.00 43.05 3.27
101 102 2.091665 CCTTGGCCATCCATCTAAACCT 60.092 50.000 6.09 0.00 43.05 3.50
102 103 3.628257 CCTTGGCCATCCATCTAAACCTT 60.628 47.826 6.09 0.00 43.05 3.50
103 104 3.017048 TGGCCATCCATCTAAACCTTG 57.983 47.619 0.00 0.00 37.47 3.61
104 105 2.580322 TGGCCATCCATCTAAACCTTGA 59.420 45.455 0.00 0.00 37.47 3.02
105 106 2.952310 GGCCATCCATCTAAACCTTGAC 59.048 50.000 0.00 0.00 0.00 3.18
106 107 2.614057 GCCATCCATCTAAACCTTGACG 59.386 50.000 0.00 0.00 0.00 4.35
107 108 3.681594 GCCATCCATCTAAACCTTGACGA 60.682 47.826 0.00 0.00 0.00 4.20
108 109 3.871594 CCATCCATCTAAACCTTGACGAC 59.128 47.826 0.00 0.00 0.00 4.34
109 110 4.503910 CATCCATCTAAACCTTGACGACA 58.496 43.478 0.00 0.00 0.00 4.35
110 111 4.819105 TCCATCTAAACCTTGACGACAT 57.181 40.909 0.00 0.00 0.00 3.06
111 112 4.755411 TCCATCTAAACCTTGACGACATC 58.245 43.478 0.00 0.00 0.00 3.06
112 113 3.551890 CCATCTAAACCTTGACGACATCG 59.448 47.826 0.00 0.00 46.33 3.84
113 114 3.226346 TCTAAACCTTGACGACATCGG 57.774 47.619 6.21 0.00 44.95 4.18
114 115 2.821378 TCTAAACCTTGACGACATCGGA 59.179 45.455 6.21 0.00 44.95 4.55
115 116 2.762535 AAACCTTGACGACATCGGAT 57.237 45.000 6.21 0.00 44.95 4.18
116 117 2.762535 AACCTTGACGACATCGGATT 57.237 45.000 6.21 0.60 44.95 3.01
117 118 3.880047 AACCTTGACGACATCGGATTA 57.120 42.857 6.21 0.00 44.95 1.75
118 119 4.402056 AACCTTGACGACATCGGATTAT 57.598 40.909 6.21 0.00 44.95 1.28
119 120 3.978687 ACCTTGACGACATCGGATTATC 58.021 45.455 6.21 0.00 44.95 1.75
120 121 3.637229 ACCTTGACGACATCGGATTATCT 59.363 43.478 6.21 0.00 44.95 1.98
121 122 4.230657 CCTTGACGACATCGGATTATCTC 58.769 47.826 6.21 0.00 44.95 2.75
122 123 3.917329 TGACGACATCGGATTATCTCC 57.083 47.619 6.21 0.00 44.95 3.71
129 130 4.580835 GGATTATCTCCGGCGAGC 57.419 61.111 9.30 0.00 35.94 5.03
130 131 1.079750 GGATTATCTCCGGCGAGCC 60.080 63.158 9.30 3.59 35.94 4.70
131 132 1.079750 GATTATCTCCGGCGAGCCC 60.080 63.158 9.30 0.00 35.94 5.19
151 152 4.660938 GCCCCACCCTCACCACAC 62.661 72.222 0.00 0.00 0.00 3.82
152 153 3.174987 CCCCACCCTCACCACACA 61.175 66.667 0.00 0.00 0.00 3.72
153 154 2.113139 CCCACCCTCACCACACAC 59.887 66.667 0.00 0.00 0.00 3.82
154 155 2.751731 CCCACCCTCACCACACACA 61.752 63.158 0.00 0.00 0.00 3.72
155 156 1.525995 CCACCCTCACCACACACAC 60.526 63.158 0.00 0.00 0.00 3.82
156 157 1.223211 CACCCTCACCACACACACA 59.777 57.895 0.00 0.00 0.00 3.72
157 158 1.095228 CACCCTCACCACACACACAC 61.095 60.000 0.00 0.00 0.00 3.82
158 159 1.223211 CCCTCACCACACACACACA 59.777 57.895 0.00 0.00 0.00 3.72
159 160 1.095228 CCCTCACCACACACACACAC 61.095 60.000 0.00 0.00 0.00 3.82
160 161 0.392327 CCTCACCACACACACACACA 60.392 55.000 0.00 0.00 0.00 3.72
161 162 0.726827 CTCACCACACACACACACAC 59.273 55.000 0.00 0.00 0.00 3.82
162 163 0.035458 TCACCACACACACACACACA 59.965 50.000 0.00 0.00 0.00 3.72
163 164 0.167908 CACCACACACACACACACAC 59.832 55.000 0.00 0.00 0.00 3.82
164 165 1.295357 ACCACACACACACACACACG 61.295 55.000 0.00 0.00 0.00 4.49
165 166 1.225991 CACACACACACACACACGC 60.226 57.895 0.00 0.00 0.00 5.34
166 167 2.021243 CACACACACACACACGCG 59.979 61.111 3.53 3.53 0.00 6.01
167 168 3.860125 ACACACACACACACGCGC 61.860 61.111 5.73 0.00 0.00 6.86
168 169 4.918060 CACACACACACACGCGCG 62.918 66.667 30.96 30.96 0.00 6.86
221 222 4.659172 CCTTTGCCTGGGACGCCA 62.659 66.667 0.00 0.00 0.00 5.69
225 226 2.741486 TTTGCCTGGGACGCCACTAC 62.741 60.000 0.00 0.00 0.00 2.73
226 227 3.391382 GCCTGGGACGCCACTACT 61.391 66.667 0.00 0.00 0.00 2.57
235 236 2.224217 CGCCACTACTGCATCGTCG 61.224 63.158 0.00 0.00 0.00 5.12
259 260 1.269936 ACTTGTAGTTGTTCCCGTCCG 60.270 52.381 0.00 0.00 0.00 4.79
326 327 0.451783 CGCTAATGCCCAGTTCAACC 59.548 55.000 0.00 0.00 35.36 3.77
332 333 1.971167 GCCCAGTTCAACCGATGCA 60.971 57.895 0.00 0.00 0.00 3.96
383 384 9.928618 TCCATCCCACAATATAAGACATTTTTA 57.071 29.630 0.00 0.00 0.00 1.52
445 446 7.827701 GTCTTATATTATGAGACGATGTGGGA 58.172 38.462 11.50 0.00 36.39 4.37
446 447 8.470805 GTCTTATATTATGAGACGATGTGGGAT 58.529 37.037 11.50 0.00 36.39 3.85
447 448 9.695155 TCTTATATTATGAGACGATGTGGGATA 57.305 33.333 0.00 0.00 0.00 2.59
501 503 7.865706 AGACTTTAATGTGCAATACTTAGGG 57.134 36.000 0.00 0.00 0.00 3.53
527 529 6.674694 CATCTAGATGTGCTTAGCAAAACT 57.325 37.500 22.42 10.68 41.47 2.66
528 530 6.484540 CATCTAGATGTGCTTAGCAAAACTG 58.515 40.000 22.42 7.38 41.47 3.16
529 531 5.793817 TCTAGATGTGCTTAGCAAAACTGA 58.206 37.500 16.03 9.27 41.47 3.41
555 559 7.704789 TTTTTAGAGTCGTTTTCAGGTACTC 57.295 36.000 0.00 0.00 34.60 2.59
561 565 1.403780 CGTTTTCAGGTACTCCCTCCG 60.404 57.143 0.00 0.00 43.86 4.63
581 585 9.392259 CCCTCCGTTTCTAAATATAAGTCTTTT 57.608 33.333 0.00 0.00 0.00 2.27
612 616 4.590850 TCATAGTGACAAGATCCCGATG 57.409 45.455 0.00 0.00 0.00 3.84
625 629 8.904834 ACAAGATCCCGATGTATATAGACATAC 58.095 37.037 12.82 6.46 40.18 2.39
694 698 7.499321 TTAGAATCTCTATCGAACAGGACTC 57.501 40.000 0.00 0.00 0.00 3.36
704 708 3.114065 CGAACAGGACTCGTATTTAGGC 58.886 50.000 0.00 0.00 0.00 3.93
768 791 5.884792 ACATGAGAAATAGCAAGGGAGAAAG 59.115 40.000 0.00 0.00 0.00 2.62
1212 1235 3.369997 CCAAGGGTAAAGAGCTCTCCTTC 60.370 52.174 24.58 12.95 32.89 3.46
1887 1910 1.451207 CGGGTTTGATGATCGGCCA 60.451 57.895 2.24 0.00 0.00 5.36
2019 2042 6.625362 AGACGCCAATCATGACATACTATAG 58.375 40.000 0.00 0.00 0.00 1.31
2102 2125 8.613060 TGCAGAGAATTGGTGAGATTTATATC 57.387 34.615 0.00 0.00 0.00 1.63
2140 2186 9.834628 TTCAGAATTTGGTAAATTGTCGTAATC 57.165 29.630 4.42 0.00 40.97 1.75
2197 2243 4.378874 GCGATCATTAGGCATTTCTTAGGC 60.379 45.833 0.00 0.00 0.00 3.93
2204 2250 4.516652 AGGCATTTCTTAGGCAAGATCT 57.483 40.909 0.00 0.00 40.47 2.75
2488 2534 8.044908 AGAAAAATTTCAGCCTTATGCATGAAT 58.955 29.630 10.16 0.00 39.61 2.57
2518 2564 5.475719 CACAATTTGTGCATCTCCTTGATT 58.524 37.500 16.05 0.00 41.89 2.57
2961 3136 5.692204 CCCTGTTATCATAAGTGACGACATC 59.308 44.000 0.00 0.00 37.14 3.06
2970 3145 2.413765 GACGACATCGAGCTCCCC 59.586 66.667 8.47 0.00 43.02 4.81
3051 3226 7.255277 GCTATTAAAAAGGGCTACTTGATGAGG 60.255 40.741 0.00 0.00 39.96 3.86
3653 3828 3.620374 AGCTCAGAATGTATGTTTGCTCG 59.380 43.478 0.00 0.00 37.40 5.03
3714 3890 2.027561 CCCCGTCTGGAATTAGTTGTCA 60.028 50.000 0.00 0.00 37.49 3.58
3726 3912 9.913310 TGGAATTAGTTGTCACATAAATGGATA 57.087 29.630 0.00 0.00 0.00 2.59
3758 3944 9.553064 AATATGTCTTGATACACTCATTTCTCC 57.447 33.333 0.00 0.00 32.72 3.71
3766 3952 2.749621 ACACTCATTTCTCCGAAATGGC 59.250 45.455 22.11 0.00 38.00 4.40
3785 3971 9.651913 GAAATGGCTAAAAATGGATGACTAAAA 57.348 29.630 0.00 0.00 0.00 1.52
4096 7705 9.994432 GGTTGTTTGATTCATAAGATTGAGTAG 57.006 33.333 0.00 0.00 0.00 2.57
4175 7785 9.617975 CATTTACTCAAAACCTTTTTGCAAAAA 57.382 25.926 29.97 29.97 36.53 1.94
4223 7833 4.294347 TCAAACAACCCAAAATCCTTCCT 58.706 39.130 0.00 0.00 0.00 3.36
4226 7836 4.463050 ACAACCCAAAATCCTTCCTGTA 57.537 40.909 0.00 0.00 0.00 2.74
4227 7837 4.149598 ACAACCCAAAATCCTTCCTGTAC 58.850 43.478 0.00 0.00 0.00 2.90
4232 7842 3.365969 CCAAAATCCTTCCTGTACGTTGC 60.366 47.826 0.00 0.00 0.00 4.17
4249 7859 1.270968 GCGATGAGCGTGACATTCG 59.729 57.895 0.00 0.00 43.41 3.34
4250 7860 1.139816 GCGATGAGCGTGACATTCGA 61.140 55.000 0.00 0.00 43.41 3.71
4252 7862 1.854743 CGATGAGCGTGACATTCGAAT 59.145 47.619 4.39 4.39 34.64 3.34
4253 7863 2.097685 CGATGAGCGTGACATTCGAATC 60.098 50.000 7.92 0.00 34.64 2.52
4254 7864 1.640428 TGAGCGTGACATTCGAATCC 58.360 50.000 7.92 3.92 0.00 3.01
4255 7865 1.067213 TGAGCGTGACATTCGAATCCA 60.067 47.619 7.92 6.67 0.00 3.41
4256 7866 1.999735 GAGCGTGACATTCGAATCCAA 59.000 47.619 7.92 0.00 0.00 3.53
4257 7867 2.609459 GAGCGTGACATTCGAATCCAAT 59.391 45.455 7.92 0.00 0.00 3.16
4258 7868 2.609459 AGCGTGACATTCGAATCCAATC 59.391 45.455 7.92 4.64 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.323629 CGGTCTGGTTGGTGGTATGT 59.676 55.000 0.00 0.00 0.00 2.29
1 2 1.024579 GCGGTCTGGTTGGTGGTATG 61.025 60.000 0.00 0.00 0.00 2.39
2 3 1.298667 GCGGTCTGGTTGGTGGTAT 59.701 57.895 0.00 0.00 0.00 2.73
3 4 2.745037 GCGGTCTGGTTGGTGGTA 59.255 61.111 0.00 0.00 0.00 3.25
4 5 4.265056 GGCGGTCTGGTTGGTGGT 62.265 66.667 0.00 0.00 0.00 4.16
5 6 2.589157 TAGGCGGTCTGGTTGGTGG 61.589 63.158 0.00 0.00 0.00 4.61
6 7 1.375523 GTAGGCGGTCTGGTTGGTG 60.376 63.158 0.00 0.00 0.00 4.17
7 8 1.535687 AGTAGGCGGTCTGGTTGGT 60.536 57.895 0.00 0.00 0.00 3.67
8 9 1.218316 GAGTAGGCGGTCTGGTTGG 59.782 63.158 0.00 0.00 0.00 3.77
9 10 0.537188 ATGAGTAGGCGGTCTGGTTG 59.463 55.000 0.00 0.00 0.00 3.77
10 11 0.537188 CATGAGTAGGCGGTCTGGTT 59.463 55.000 0.00 0.00 0.00 3.67
11 12 1.330655 CCATGAGTAGGCGGTCTGGT 61.331 60.000 0.00 0.00 0.00 4.00
12 13 1.443407 CCATGAGTAGGCGGTCTGG 59.557 63.158 0.00 0.00 0.00 3.86
13 14 1.227380 GCCATGAGTAGGCGGTCTG 60.227 63.158 0.00 0.00 43.15 3.51
14 15 3.221222 GCCATGAGTAGGCGGTCT 58.779 61.111 0.00 0.00 43.15 3.85
31 32 1.528824 CACCTCTAGCCACATGGGG 59.471 63.158 10.61 10.61 37.04 4.96
32 33 1.153086 GCACCTCTAGCCACATGGG 60.153 63.158 0.00 0.00 40.85 4.00
33 34 0.179062 GAGCACCTCTAGCCACATGG 60.179 60.000 0.00 0.00 38.53 3.66
34 35 0.829333 AGAGCACCTCTAGCCACATG 59.171 55.000 0.00 0.00 39.28 3.21
35 36 1.209019 CAAGAGCACCTCTAGCCACAT 59.791 52.381 0.00 0.00 40.28 3.21
36 37 0.610174 CAAGAGCACCTCTAGCCACA 59.390 55.000 0.00 0.00 40.28 4.17
37 38 0.742635 GCAAGAGCACCTCTAGCCAC 60.743 60.000 0.00 0.00 40.28 5.01
38 39 1.599047 GCAAGAGCACCTCTAGCCA 59.401 57.895 0.00 0.00 40.28 4.75
39 40 4.530581 GCAAGAGCACCTCTAGCC 57.469 61.111 0.00 0.00 40.28 3.93
50 51 3.184683 GCGAGGCTCGTGCAAGAG 61.185 66.667 34.41 23.37 42.81 2.85
51 52 4.742201 GGCGAGGCTCGTGCAAGA 62.742 66.667 34.41 1.47 42.81 3.02
84 85 2.952310 GTCAAGGTTTAGATGGATGGCC 59.048 50.000 0.00 0.00 0.00 5.36
85 86 2.614057 CGTCAAGGTTTAGATGGATGGC 59.386 50.000 0.00 0.00 0.00 4.40
86 87 3.871594 GTCGTCAAGGTTTAGATGGATGG 59.128 47.826 0.00 0.00 0.00 3.51
87 88 4.503910 TGTCGTCAAGGTTTAGATGGATG 58.496 43.478 0.00 0.00 0.00 3.51
88 89 4.819105 TGTCGTCAAGGTTTAGATGGAT 57.181 40.909 0.00 0.00 0.00 3.41
89 90 4.676986 CGATGTCGTCAAGGTTTAGATGGA 60.677 45.833 0.00 0.00 34.11 3.41
90 91 3.551890 CGATGTCGTCAAGGTTTAGATGG 59.448 47.826 0.00 0.00 34.11 3.51
91 92 3.551890 CCGATGTCGTCAAGGTTTAGATG 59.448 47.826 1.44 0.00 37.74 2.90
92 93 3.446161 TCCGATGTCGTCAAGGTTTAGAT 59.554 43.478 1.44 0.00 37.74 1.98
93 94 2.821378 TCCGATGTCGTCAAGGTTTAGA 59.179 45.455 1.44 0.00 37.74 2.10
94 95 3.226346 TCCGATGTCGTCAAGGTTTAG 57.774 47.619 1.44 0.00 37.74 1.85
95 96 3.880047 ATCCGATGTCGTCAAGGTTTA 57.120 42.857 1.44 0.00 37.74 2.01
96 97 2.762535 ATCCGATGTCGTCAAGGTTT 57.237 45.000 1.44 0.00 37.74 3.27
97 98 2.762535 AATCCGATGTCGTCAAGGTT 57.237 45.000 1.44 0.00 37.74 3.50
98 99 3.637229 AGATAATCCGATGTCGTCAAGGT 59.363 43.478 1.44 0.00 37.74 3.50
99 100 4.230657 GAGATAATCCGATGTCGTCAAGG 58.769 47.826 1.44 2.12 37.74 3.61
100 101 4.230657 GGAGATAATCCGATGTCGTCAAG 58.769 47.826 1.44 0.00 38.67 3.02
101 102 4.238761 GGAGATAATCCGATGTCGTCAA 57.761 45.455 1.44 0.00 38.67 3.18
102 103 3.917329 GGAGATAATCCGATGTCGTCA 57.083 47.619 1.44 0.00 38.67 4.35
112 113 1.079750 GGCTCGCCGGAGATAATCC 60.080 63.158 8.83 4.32 43.27 3.01
113 114 1.079750 GGGCTCGCCGGAGATAATC 60.080 63.158 8.83 0.00 43.27 1.75
114 115 2.932234 CGGGCTCGCCGGAGATAAT 61.932 63.158 8.83 0.00 43.27 1.28
115 116 3.602677 CGGGCTCGCCGGAGATAA 61.603 66.667 8.83 0.00 43.27 1.75
134 135 4.660938 GTGTGGTGAGGGTGGGGC 62.661 72.222 0.00 0.00 0.00 5.80
135 136 3.174987 TGTGTGGTGAGGGTGGGG 61.175 66.667 0.00 0.00 0.00 4.96
136 137 2.113139 GTGTGTGGTGAGGGTGGG 59.887 66.667 0.00 0.00 0.00 4.61
137 138 1.525995 GTGTGTGTGGTGAGGGTGG 60.526 63.158 0.00 0.00 0.00 4.61
138 139 1.095228 GTGTGTGTGTGGTGAGGGTG 61.095 60.000 0.00 0.00 0.00 4.61
139 140 1.223487 GTGTGTGTGTGGTGAGGGT 59.777 57.895 0.00 0.00 0.00 4.34
140 141 1.095228 GTGTGTGTGTGTGGTGAGGG 61.095 60.000 0.00 0.00 0.00 4.30
141 142 0.392327 TGTGTGTGTGTGTGGTGAGG 60.392 55.000 0.00 0.00 0.00 3.86
142 143 0.726827 GTGTGTGTGTGTGTGGTGAG 59.273 55.000 0.00 0.00 0.00 3.51
143 144 0.035458 TGTGTGTGTGTGTGTGGTGA 59.965 50.000 0.00 0.00 0.00 4.02
144 145 0.167908 GTGTGTGTGTGTGTGTGGTG 59.832 55.000 0.00 0.00 0.00 4.17
145 146 1.295357 CGTGTGTGTGTGTGTGTGGT 61.295 55.000 0.00 0.00 0.00 4.16
146 147 1.423450 CGTGTGTGTGTGTGTGTGG 59.577 57.895 0.00 0.00 0.00 4.17
147 148 1.225991 GCGTGTGTGTGTGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
148 149 2.735677 CGCGTGTGTGTGTGTGTGT 61.736 57.895 0.00 0.00 0.00 3.72
149 150 2.021243 CGCGTGTGTGTGTGTGTG 59.979 61.111 0.00 0.00 0.00 3.82
150 151 3.860125 GCGCGTGTGTGTGTGTGT 61.860 61.111 8.43 0.00 0.00 3.72
151 152 4.918060 CGCGCGTGTGTGTGTGTG 62.918 66.667 24.19 0.00 0.00 3.82
170 171 4.267013 GAAGATTCGGACGCGCGC 62.267 66.667 32.58 23.91 0.00 6.86
171 172 2.441378 TTGAAGATTCGGACGCGCG 61.441 57.895 30.96 30.96 0.00 6.86
172 173 1.058903 GTTGAAGATTCGGACGCGC 59.941 57.895 5.73 0.00 0.00 6.86
173 174 1.693083 GGGTTGAAGATTCGGACGCG 61.693 60.000 3.53 3.53 0.00 6.01
174 175 0.391263 AGGGTTGAAGATTCGGACGC 60.391 55.000 7.45 7.45 32.70 5.19
175 176 1.732259 CAAGGGTTGAAGATTCGGACG 59.268 52.381 0.00 0.00 0.00 4.79
176 177 1.468914 GCAAGGGTTGAAGATTCGGAC 59.531 52.381 0.00 0.00 0.00 4.79
177 178 1.613255 GGCAAGGGTTGAAGATTCGGA 60.613 52.381 0.00 0.00 0.00 4.55
178 179 0.811281 GGCAAGGGTTGAAGATTCGG 59.189 55.000 0.00 0.00 0.00 4.30
179 180 0.811281 GGGCAAGGGTTGAAGATTCG 59.189 55.000 0.00 0.00 0.00 3.34
180 181 2.095461 GAGGGCAAGGGTTGAAGATTC 58.905 52.381 0.00 0.00 0.00 2.52
181 182 1.272704 GGAGGGCAAGGGTTGAAGATT 60.273 52.381 0.00 0.00 0.00 2.40
182 183 0.332972 GGAGGGCAAGGGTTGAAGAT 59.667 55.000 0.00 0.00 0.00 2.40
183 184 1.767692 GGAGGGCAAGGGTTGAAGA 59.232 57.895 0.00 0.00 0.00 2.87
184 185 1.304464 GGGAGGGCAAGGGTTGAAG 60.304 63.158 0.00 0.00 0.00 3.02
185 186 2.851045 GGGAGGGCAAGGGTTGAA 59.149 61.111 0.00 0.00 0.00 2.69
208 209 3.702048 GTAGTGGCGTCCCAGGCA 61.702 66.667 0.00 0.00 43.18 4.75
211 212 2.125512 GCAGTAGTGGCGTCCCAG 60.126 66.667 0.00 0.00 43.18 4.45
221 222 0.736325 GTTGGCGACGATGCAGTAGT 60.736 55.000 0.00 0.00 36.28 2.73
225 226 1.133253 CAAGTTGGCGACGATGCAG 59.867 57.895 0.00 0.00 36.28 4.41
226 227 0.319986 TACAAGTTGGCGACGATGCA 60.320 50.000 7.96 0.00 36.28 3.96
259 260 4.893601 GGAACGGCGGCTAGGCTC 62.894 72.222 13.24 6.19 44.22 4.70
280 281 3.313750 CGCTAATCGCAGTGAGGC 58.686 61.111 0.00 0.00 39.08 4.70
319 320 5.905480 AAAAGATTTTGCATCGGTTGAAC 57.095 34.783 0.00 0.00 0.00 3.18
477 479 6.318900 GCCCTAAGTATTGCACATTAAAGTCT 59.681 38.462 0.00 0.00 0.00 3.24
480 482 6.449635 TGCCCTAAGTATTGCACATTAAAG 57.550 37.500 0.00 0.00 0.00 1.85
507 509 6.674694 ATCAGTTTTGCTAAGCACATCTAG 57.325 37.500 0.00 0.00 38.71 2.43
555 559 8.959705 AAAGACTTATATTTAGAAACGGAGGG 57.040 34.615 0.00 0.00 0.00 4.30
586 590 7.119709 TCGGGATCTTGTCACTATGAAAATA 57.880 36.000 0.00 0.00 0.00 1.40
593 597 7.962995 ATATACATCGGGATCTTGTCACTAT 57.037 36.000 0.00 0.00 0.00 2.12
597 601 6.946009 TGTCTATATACATCGGGATCTTGTCA 59.054 38.462 0.00 0.00 0.00 3.58
598 602 7.392494 TGTCTATATACATCGGGATCTTGTC 57.608 40.000 0.00 0.00 0.00 3.18
682 686 3.181493 GCCTAAATACGAGTCCTGTTCGA 60.181 47.826 1.31 0.00 40.36 3.71
684 688 3.455327 GGCCTAAATACGAGTCCTGTTC 58.545 50.000 0.00 0.00 0.00 3.18
687 691 1.269621 CCGGCCTAAATACGAGTCCTG 60.270 57.143 0.00 0.00 0.00 3.86
694 698 2.320745 AAACTCCCGGCCTAAATACG 57.679 50.000 0.00 0.00 0.00 3.06
768 791 1.545582 TGTAGCAGCAGCCAATTTTCC 59.454 47.619 0.00 0.00 43.56 3.13
1212 1235 1.450531 GGCGGCCATTCTCATCAAGG 61.451 60.000 15.62 0.00 0.00 3.61
1887 1910 4.777463 CTCCCCGGAAGTATAACAATGTT 58.223 43.478 0.73 3.43 0.00 2.71
2019 2042 1.202076 GCGAGAATTAAGCAGTGCCAC 60.202 52.381 12.58 0.00 0.00 5.01
2102 2125 7.076842 ACCAAATTCTGAATTATGTCACTCG 57.923 36.000 15.45 6.01 0.00 4.18
2140 2186 4.582701 AGAGTCTCAGCCTAATGATTCG 57.417 45.455 1.94 0.00 0.00 3.34
2204 2250 8.408043 TCAAAGCTGGAATTCTGAAATCTTAA 57.592 30.769 5.23 0.00 0.00 1.85
2468 2514 5.508489 CCGAATTCATGCATAAGGCTGAAAT 60.508 40.000 0.00 0.00 45.15 2.17
2518 2564 3.197549 TGCACAACATCTATCTACCAGCA 59.802 43.478 0.00 0.00 0.00 4.41
2961 3136 0.036448 TATCCTCGTAGGGGAGCTCG 59.964 60.000 7.83 0.00 35.59 5.03
2970 3145 9.451002 TTTGAATAGTCTAGGATATCCTCGTAG 57.549 37.037 27.86 19.15 44.77 3.51
3051 3226 7.096477 CGATGCTTGTTTATGCCTTTAATTAGC 60.096 37.037 0.00 0.00 0.00 3.09
3700 3876 8.821686 ATCCATTTATGTGACAACTAATTCCA 57.178 30.769 0.00 0.00 0.00 3.53
3748 3934 5.818136 TTTAGCCATTTCGGAGAAATGAG 57.182 39.130 27.34 20.19 45.90 2.90
3758 3944 5.894807 AGTCATCCATTTTTAGCCATTTCG 58.105 37.500 0.00 0.00 0.00 3.46
4175 7785 9.729281 ATTGCAACATAGGAAAAATGAAGAATT 57.271 25.926 0.00 0.00 0.00 2.17
4183 7793 8.558700 GTTGTTTGATTGCAACATAGGAAAAAT 58.441 29.630 0.00 0.00 43.03 1.82
4223 7833 1.081041 ACGCTCATCGCAACGTACA 60.081 52.632 0.00 0.00 43.23 2.90
4226 7836 2.049526 TCACGCTCATCGCAACGT 60.050 55.556 0.00 0.00 43.23 3.99
4227 7837 1.686566 ATGTCACGCTCATCGCAACG 61.687 55.000 0.00 0.00 43.23 4.10
4232 7842 1.268265 TTCGAATGTCACGCTCATCG 58.732 50.000 0.00 0.00 45.38 3.84


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.